An efficient computational method for screening functional SNPs in plants

Kharabian, Ardashir

doi:10.1016/j.jtbi.2010.04.017

Cited by 14 publications

(14 citation statements)

References 45 publications

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“…Also for Zhen Shang 47 and Alinano C, SNP mutations were identified in the non-coding sequences: 2 in the promoter region, 11 in intron 1, 1 in intron 6, 9 in intron 10 and 2 in intron 12 (Figure 2; Table 4). Most of the SNPs identified in the present work are not classified in the group of SNPs computationally characterized by Kharabian (2010) and present in OryzaSNP (http://oryzasnp.plantbiology.msu.edu/cgi-bin/gbrowse/osa_snp_tigr/) and dbSNP (http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp&TAbCmd=Limits) databases. Additionally to these SNPs polymorphisms, a 4 bp tandem repeat that was identified in rice cvs.…”

Section: Resultsmentioning

confidence: 99%

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Biselli¹,

Cavalluzzo²,

Perrini³

et al. 2014

Rice

136

126

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BackgroundApparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited.ResultsIn this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers.ConclusionsThe addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.

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Section: Resultsmentioning

confidence: 99%

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Biselli¹,

Cavalluzzo²,

Perrini³

et al. 2014

Rice

136

126

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“…On the other hand, the SNP effects on protein functions were inferred by modelled structures because the molecular modelling method has been found useful for estimating the effects of the substitution of amino acid residues on protein function. 6,31 Therefore, homology modelling was applied to the tomato genes with cSNPs. As a result, it was predicted that the protein functions (or catalytic activities) of the 200 genes might be altered by the substitutions because the SNPs were located on the candidate functional sites.…”

Section: Resultsmentioning

confidence: 99%

“…5 In plants, the functional SNPs on ‘granule bound starch synthase I’ ( GBSSI ) have been screened by computational analyses including sequence alignments and the modelling of three-dimensional structures. 6 …”

Section: Introductionmentioning

confidence: 99%

Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

et al. 2013

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The genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F1 hybrids, and wild relatives, were collected using Illumina's Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI's eukaryotic orthologous groups (KOG). To infer the SNPs' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database ().

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“…Cancer, diabetes and obesity are considered prototypical systems-diseases in which the systems biologists are gathering novel insights [2]. The emergence of high throughput technologies to analyse complex sets of data in both plant and animal models has used computational algorithms [4].…”

Section: Introductionmentioning

confidence: 99%

Systems Biology Approaches Towards the Prediction of Prospective Novel Plant System-Derived Products or Services

Vishnu¹

2013

J Comput Sci Syst Biol

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An efficient computational method for screening functional SNPs in plants

Cited by 14 publications

References 45 publications

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

Systems Biology Approaches Towards the Prediction of Prospective Novel Plant System-Derived Products or Services

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